[MMTK] PSF file generation anyone?

Lutz.Ehrlich@EMBL-Heidelberg.de Lutz.Ehrlich@EMBL-Heidelberg.de
Wed, 21 Jul 1999 14:15:48 +0200 (MDT)

Konrad Hinsen writes:
> > has anybody written some code to generate PSF files from MMTK universe 
> > objects using a CHARMM topology file? I'm using PSF files generated by 
> Not me! And I am not even sure that this is doable without a major
> effort; you'd have to parse the CHARMM topoloy files first and then
> somehow match the MMTK objects to CHARMM residues, which use
> different atom names etc. Sounds like a rather unpleasant task.

Yeah, right. Some of it (Partial parsing of XPLOR topology files, atom
name reconversion, and validation against a PSF file) is solved
already. As a first temporary solution, I thought about using XPLOR to 
generate the PSF on the fly (the atoms need to be properly named for
that). This is messy as every single peptide chains needs its own PDB
file, but it's doable.

> > XPLOR right now, but this might become unwieldy as soon as I have to
> > add/delete certain atoms from one simulation to the next...
> I don't understand what you are trying to do. Maybe there is a simpler
> solution!

Well, I don't think so. As part of my protein-protein docking
simulations, the number of molecules might change if inteface water
molecules are introduced. As I run lots of short simulations
consecutively with XPLOR, I'll have to generate the proper XPLOR input 
on the fly.



Lutz Ehrlich		 	http://www.embl-heidelberg.de/~ehrlich

European Molecular Biology Laboratory		phone: +49-6221-387-140
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